DTU Systembiologi
DTU Biosustain
Henrik Bjørn Nielsen

Henrik Bjørn Nielsen

Associate professor

Department of Systems Biology

Center for Biological Sequence Analysis

Technical University of Denmark

Kemitorvet

Building 208, room 017

2800 Kgs. Lyngby

Ph.
Ph.
Fax +45 45 93 15 85
E-mail hbjorn@cbs.dtu.dk
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2014
 

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

Nielsen, Henrik Bjørn ; Almeida, Mathieu ; Juncker, Agnieszka ; Rasmussen, Simon ; Li, Junhua ; Sunagawa, Shinichi ; Plichta, Damian Rafal ; Gautier, Laurent ; Pedersen, Anders Gorm ; Emmanuelle, Le Chatelier ; Pelletier, Eric ; Bonde, Ida ; Nielsen, Trine ; Manichanh, Chaysavanh ; Arumugam, Manimozhiyan ; Batto, Jean-Michel ; dos Santos, Marcelo Bertalan Quintanilha ; Blom, Nikolaj ; Borruel, Natalia ; Burgdorf, Kristoffer S. ; Boumezbeur, Fouad ; Casellas, Francesc ; Doré, Joël ; Dworzynski, Piotr ; Guarner, Francisco ; Hansen, Torben ; Hildebrand, Falk ; Kaas, Rolf Sommer ; Kennedy, Sean ; Kristiansen, Karsten ; Kultima, Jens Roat ; Léonard, Pierre ; Levenez, Florence ; Lund, Ole ; Moumen, Bouziane ; Denis, Le Paslier ; Pons, Nicolas ; Pedersen, Oluf ; Prifti, Edi ; Qin, Junjie ; Raes, Jeroen ; Sørensen, Søren ; Tap, Julien ; Tims, Sebastian ; Ussery, David ; Yamada, Takuji ; Renault, Pierre ; Sicheritz-Pontén, Thomas ; Bork, Peer ; Wang, Jun ; Brunak, Søren ; Ehrlich, S. Dusko
in journal: Nature Biotechnology (ISSN: 1087-0156) (DOI: http://dx.doi.org/10.1038/nbt.2939), 2014

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2014     |    DOI: http://dx.doi.org/10.1038/nbt.2939

2013
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The chemical interactome space between the human host and the genetically defined gut metabotypes

Jacobsen, Ulrik Plesner ; Nielsen, Henrik Bjørn ; Hildebrand, Falk ; Raes, Jeroen ; Sicheritz-Pontén, Thomas ; Kouskoumvekaki, Irene ; Panagiotou, Gianni
in journal: I S M E Journal (ISSN: 1751-7362) (DOI: http://dx.doi.org/10.1038/ismej.2012.141), vol: 7, pages: 730-742, 2013

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2013     |    DOI: http://dx.doi.org/10.1038/ismej.2012.141

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Transcriptome Responses to Combinations of Stresses in Arabidopsis

Rasmussen, Simon ; Barah, Pankaj ; Suarez-Rodriguez, Maria Cristina ; Bressendorff, Simon ; Friis, Pia ; Costantino, Paolo ; Bones, Atle M. ; Nielsen, Henrik Bjørn ; Mundy, John
in journal: Plant Physiology (ISSN: 0032-0889) (DOI: http://dx.doi.org/10.1104/pp.112.210773), vol: 161, issue: 4, pages: 1783-1794, 2013

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2013     |    DOI: http://dx.doi.org/10.1104/pp.112.210773

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Transcriptome profiling of mice testes following low dose irradiation

Belling, Kirstine C. ; Tanaka, Masami ; Dalgaard, Marlene Danner ; Nielsen, John Erik ; Nielsen, Henrik Bjørn ; Brunak, Søren ; Almstrup, Kristian ; Leffers, Henrik
in journal: Reproductive Biology and Endocrinology (ISSN: 14777827) (DOI: http://dx.doi.org/10.1186/1477-7827-11-50), vol: 11, issue: 1, 2013

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2013     |    DOI: http://dx.doi.org/10.1186/1477-7827-11-50

 

TIMP1 overexpression mediates resistance of MCF-7 human breast cancer cells to fulvestrant and down-regulates progesterone receptor expression

Bjerre, Christina ; Vinther, Lena ; Belling, Kirstine C. ; Würtz, Sidse Ø. ; Yadav, Rachita ; Lademan, Ulrik ; Rigina, Olga ; Nguyen Do, Khoa ; Ditzel, Henrik Jørn ; Lykkesfeldt, Anne Elisabeth ; Wang, Jun ; Nielsen, Henrik Bjørn ; Brünner, Nils ; Gupta, Ramneek ; Schrohl, Anne-Sofie ; Stenvang, Jan
in journal: Tumor Biology (ISSN: 1010-4283) (DOI: http://dx.doi.org/10.1007/s13277-013-0969-7), vol: 34, pages: 3839-3851, 2013

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2013     |    DOI: http://dx.doi.org/10.1007/s13277-013-0969-7

 

Richness of human gut microbiome correlates with metabolic markers.

Le Chatelier, Emmanuelle ; Nielsen, Trine ; Qin, Junjie ; Prifti, Edi ; Hildebrand, Falk ; Falony, Gwen ; Almeida, Mathieu ; Arumugam, Manimozhiyan ; Batto, Jean-Michel ; Kennedy, Sean ; Leonard, Pierre ; Li, Junhua ; Burgdorf, Kristoffer ; Grarup, Niels ; Jørgensen, Torben ; Brandslund, Ivan ; Nielsen, Henrik Bjørn ; Juncker, Agnieszka ; dos Santos, Marcelo Bertalan Quintanilha ; Levenez, Florence ; Pons, Nicolas ; Rasmussen, Simon ; Sunagawa, Shinichi ; Tap, Julien ; Tims, Sebastian ; Zoetendal, Erwin G ; Brunak, Søren ; Clément, Karine ; Doré, Joël ; Kleerebezem, Michiel ; Kristiansen, Karsten ; Renault, Pierre ; Sicheritz-Pontén, Thomas ; de Vos, Willem M. ; Zucker, Jean-Daniel ; Raes, Jeroen ; Hansen, Torben ; Bork, Peer ; Wang, Jun ; Ehrlich, S Dusko ; Pedersen, Oluf
in journal: Nature (ISSN: 00280836) (DOI: http://dx.doi.org/10.1038/nature12506), vol: 500, issue: 7464, pages: 541-546, 2013

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2013     |    DOI: http://dx.doi.org/10.1038/nature12506

 

Metagenomic species profiling using universal phylogenetic marker genes

Sunagawa, Shinichi ; Mende, Daniel R ; Zeller, Georg ; Izquierdo-Carrasco, Fernando ; Berger, Simon A ; Kultima, Jens Roat ; Coelho, Luis Pedro ; Arumugam, Manimozhiyan ; Tap, Julien ; Nielsen, Henrik Bjørn ; Rasmussen, Simon ; Brunak, Søren ; Pedersen, Oluf ; Guarner, Francisco ; de Vos, Willem M ; Wang, Jun ; Li, Junhua ; Doré, Joël ; Ehrlich, S Dusko ; Stamatakis, Alexandros ; Bork, Peer
in journal: Nature Methods (ISSN: 15487091) (DOI: http://dx.doi.org/10.1038/nmeth.2693), vol: 10, issue: 12, pages: 1196–1199, 2013

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2013     |    DOI: http://dx.doi.org/10.1038/nmeth.2693

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Genome-scale cold stress response regulatory networks in ten Arabidopsis thaliana ecotypes

Barah, Pankaj ; Jayavelu, Naresh Doni ; Rasmussen, Simon ; Nielsen, Henrik Bjørn ; Mundy, John ; Bones, Atle M
in journal: BMC Genomics (ISSN: 14712164) (DOI: http://dx.doi.org/10.1186/1471-2164-14-722), vol: 14, issue: 1, pages: 722, 2013

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2013     |    DOI: http://dx.doi.org/10.1186/1471-2164-14-722

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Metagenomic Analysis of the Human Gut Microbiome

dos Santos, Marcelo Bertalan Quintanilha ; Nielsen, Henrik Bjørn (Supervisor) ; Sicheritz-Pontén, Thomas (Main supervisor)
Technical University of Denmark, pages: 117

Type: Ph.D. thesis

Status: Published     |    Year: 2013

2012
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A comparative analysis of the intestinal metagenomes present in guinea pigs (Cavia porcellus) and humans (Homo sapiens)

Hildebrand, Falk ; Ebersbach, Tine ; Nielsen, Henrik Bjørn ; Li, Xiaoping ; Sonne, Si Brask ; dos Santos, Marcelo Bertalan Quintanilha ; Dimitrov, Peter ; Madsen, Lise ; Qin, Junjie ; Wang, Jun ; Raes, Jeroen ; Kristiansen, Karsten ; Licht, Tine Rask
in journal: B M C Genomics (ISSN: 1471-2164) (DOI: http://dx.doi.org/10.1186/1471-2164-13-514), vol: 13, issue: 514, 2012

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2012     |    DOI: http://dx.doi.org/10.1186/1471-2164-13-514